PDBx/mmCIF
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Data Category refine

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General

Category name
refine
Required in PDB entries
no
Category group membership
refine_group
Used in current PDB entries
Yes, in about 89.4 % of entries

Category Relationship Diagrams

70
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70
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Category Description 

               Data items in the REFINE category record details about the
               structure-refinement parameters.

Category Examples

2

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Category Example1

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    _refine.entry_id                       '5HVP'
    _refine.ls_number_reflns_obs           12901
    _refine.ls_number_restraints           6609
    _refine.ls_number_parameters           7032
    _refine.ls_R_factor_obs                0.176
    _refine.ls_weighting_scheme            calc
    _refine.ls_weighting_details
    ; Sigdel model of Konnert-Hendrickson:
      Sigdel: Afsig +  Bfsig*(sin(theta)/lambda-1/6)
      Afsig = 22.0, Bfsig = -150.0 at beginning of refinement
      Afsig = 15.5, Bfsig =  -50.0 at end of refinement
    ;

Category Example2

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    _refine.details              sfls:_F_calc_weight_full_matrix

    _refine.ls_structure_factor_coef   F
    _refine.ls_matrix_type             full
    _refine.ls_weighting_scheme   calc
    _refine.ls_weighting_details  'w=1/(\s^2^(F)+0.0004F^2^)'
    _refine.ls_hydrogen_treatment     'refxyz except H332B noref'
    _refine.ls_extinction_method       Zachariasen
    _refine.ls_extinction_coef         3514
    _refine.ls_extinction_expression
    ; Larson, A. C. (1970). "Crystallographic Computing", edited
      by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.
    ;
    _refine.ls_abs_structure_details
    ; The absolute configuration was assigned to agree with the
      known chirality at C3 arising from its precursor l-leucine.
    ;
    _refine.ls_abs_structure_Flack     0
    _refine.ls_number_reflns_obs       1408
    _refine.ls_number_parameters       272
    _refine.ls_number_restraints       0
    _refine.ls_number_constraints      0
    _refine.ls_R_factor_all               .038
    _refine.ls_R_factor_obs               .034
    _refine.ls_wR_factor_all              .044
    _refine.ls_wR_factor_obs              .042
    _refine.ls_goodness_of_fit_all       1.462
    _refine.ls_goodness_of_fit_obs       1.515
    _refine.ls_shift_over_esd_max         .535
    _refine.ls_shift_over_esd_mean        .044
    _refine.diff_density_min              -.108
    _refine.diff_density_max              .131

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